[sqlalchemy] Documenting sqlalchemy objects via sphinx automodule
I'm not sure there is a solution to this problem without changes to sphinx,
but here is what I've got. In my __init__.py, I have:
Session = sessionmaker()
Base = declarative_base()
def init_model(**kwargs):
Initialize the database model
mydb = URL(drivername='mysql',
database='solexa',
query= { 'read_default_file' : '~/.my.cnf' },
**kwargs)
engine = create_engine(mydb)
Session.configure(bind=engine)
Base.metadata.bind=engine
import meltzdbtools.solexa.objects as objects
Then, I have a bunch of classes in objects.py that look like:
from meltzdbtools.solexa import Base
class StudyFile(Base):
__tablename__ = 'solexa_study_file'
__table_args__ = (
ForeignKeyConstraint(['study_id'], ['solexa_study.ID']),
ForeignKeyConstraint(['basecalllane_id'],
['solexa_file.BasecallLane_ID']),
ForeignKeyConstraint(['library_id'], ['solexa_file.Library_ID']),
{autoload:True})
study = relationship('Study')
When I try to run automodule documentation on meltzdbtools.solexa.objects,
of course init_model() has not been run, so autoloading fails and Base is
not bound to an engine. Any suggestions as to how to deal with this
problem?
Thanks,
Sean
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[sqlalchemy] Re: Cannot adapt for insert
On Oct 3, 10:58 pm, Sean Davis [EMAIL PROTECTED] wrote:
ProgrammingError: (ProgrammingError) can't adapt 'INSERT INTO
runbrowser_image (id, nobj, focusmetric, focusuniformity, choffset_x,
choffset_y, blu, flu, int_min, int_mean, int_stdev, int_max,
int_median, int_q87, nse_min, nse_mean, nse_stdev, nse_max, base,
tile_id) VALUES (%(id)s, %(nobj)s, %(focusmetric)s, %
(focusuniformity)s, %(choffset_x)s, %(choffset_y)s, %(blu)s, %(flu)s, %
(int_min)s, %(int_mean)s, %(int_stdev)s, %(int_max)s, %(int_median)s, %
(int_q87)s, %(nse_min)s, %(nse_mean)s, %(nse_stdev)s, %(nse_max)s, %
(base)s, %(tile_id)s)' {'int_q87': 6499.11498,
'focusuniformity': 95.1993894, 'nse_mean': 273.3298649998,
'int_stdev': 2763.36702, 'blu': 68.97684479995, 'nobj':
14597, 'flu': 68.2585204, 'int_min': -1874.16735,
'choffset_y': 0.0, 'choffset_x': 0.0, 'int_mean': 2965.79126, 'base':
'A', 'nse_stdev': 110.751434, 'int_median': 2022.095, 'nse_min': 0.0,
'nse_max': 732.833301, 'tile_id': 37504, 'int_max':
19389.40429998, 'id': 2L, 'focusmetric': 77.3844693}
The table is described as:
class RunBrowserImage(Base):
__tablename__ = runbrowser_image
id = Column(Integer,primary_key=True)
nobj = Column(Integer)
focusmetric = Column(Float)
focusuniformity = Column(Float)
choffset_x = Column(Float)
choffset_y = Column(Float)
blu = Column(Float)
flu = Column(Float)
int_min = Column(Float)
int_mean = Column(Float)
int_stdev = Column(Float)
int_max = Column(Float)
int_median = Column(Float)
int_q87 = Column(Float)
nse_min = Column(Float)
nse_mean = Column(Float)
nse_stdev = Column(Float)
nse_max = Column(Float)
base = Column(CHAR(1))
tile_id = Column(Integer,ForeignKey('runbrowser_tile.id'))
tile = relation(RunBrowserTile,backref=backref('images'))
I cannot figure out why the error. I know it must be something
obvious, but I can't find it.
This was due to not casting the base() column to a unicode string (or,
at least, it fixed the problem).
Sean
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[sqlalchemy] Cannot adapt for insert
ProgrammingError: (ProgrammingError) can't adapt 'INSERT INTO
runbrowser_image (id, nobj, focusmetric, focusuniformity, choffset_x,
choffset_y, blu, flu, int_min, int_mean, int_stdev, int_max,
int_median, int_q87, nse_min, nse_mean, nse_stdev, nse_max, base,
tile_id) VALUES (%(id)s, %(nobj)s, %(focusmetric)s, %
(focusuniformity)s, %(choffset_x)s, %(choffset_y)s, %(blu)s, %(flu)s, %
(int_min)s, %(int_mean)s, %(int_stdev)s, %(int_max)s, %(int_median)s, %
(int_q87)s, %(nse_min)s, %(nse_mean)s, %(nse_stdev)s, %(nse_max)s, %
(base)s, %(tile_id)s)' {'int_q87': 6499.11498,
'focusuniformity': 95.1993894, 'nse_mean': 273.3298649998,
'int_stdev': 2763.36702, 'blu': 68.97684479995, 'nobj':
14597, 'flu': 68.2585204, 'int_min': -1874.16735,
'choffset_y': 0.0, 'choffset_x': 0.0, 'int_mean': 2965.79126, 'base':
'A', 'nse_stdev': 110.751434, 'int_median': 2022.095, 'nse_min': 0.0,
'nse_max': 732.833301, 'tile_id': 37504, 'int_max':
19389.40429998, 'id': 2L, 'focusmetric': 77.3844693}
The table is described as:
class RunBrowserImage(Base):
__tablename__ = runbrowser_image
id = Column(Integer,primary_key=True)
nobj = Column(Integer)
focusmetric = Column(Float)
focusuniformity = Column(Float)
choffset_x = Column(Float)
choffset_y = Column(Float)
blu = Column(Float)
flu = Column(Float)
int_min = Column(Float)
int_mean = Column(Float)
int_stdev = Column(Float)
int_max = Column(Float)
int_median = Column(Float)
int_q87 = Column(Float)
nse_min = Column(Float)
nse_mean = Column(Float)
nse_stdev = Column(Float)
nse_max = Column(Float)
base = Column(CHAR(1))
tile_id = Column(Integer,ForeignKey('runbrowser_tile.id'))
tile = relation(RunBrowserTile,backref=backref('images'))
I cannot figure out why the error. I know it must be something
obvious, but I can't find it.
Any suggestions?
Thanks,
Sean
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[sqlalchemy] getting all indexes in a metadata instance
I am mirroring a database from mysql to postgresql. Mysql allows indexes to have the same names as columns. I would like to find all the indexes and rename them systematically to avoid these name collisions. How can I get the list of indexes and then modify the names before creating the second schema in postgres from the metadata? Thanks, Sean --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups sqlalchemy group. To post to this group, send email to sqlalchemy@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sqlalchemy?hl=en -~--~~~~--~~--~--~---
[sqlalchemy] Re: getting all indexes in a metadata instance
On Sep 30, 11:18 am, Sean Davis [EMAIL PROTECTED] wrote: I am mirroring a database from mysql to postgresql. Mysql allows indexes to have the same names as columns. I would like to find all the indexes and rename them systematically to avoid these name collisions. How can I get the list of indexes and then modify the names before creating the second schema in postgres from the metadata? Got it. Loop over the tables and the indexes are in table.indexes. Sean --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups sqlalchemy group. To post to this group, send email to sqlalchemy@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sqlalchemy?hl=en -~--~~~~--~~--~--~---
[sqlalchemy] Custom type definition and can't adapt 'INSERT INTO.... error
I have been playing with new types using sqlalchemy and have an error
I do not understand. Table schema and type definition are here:
-
def generate_uuid():
return uuid.uuid1()
class GUID(sa.types.TypeEngine):
def __init__(self):
pass
def get_col_spec(self):
return varchar(40)
def convert_bind_param(self, value, engine):
return str(value)
def convert_result_value(self, value, engine):
return uuid.UUID(value)
t_contacts = sa.Table('contacts',meta.metadata,
sa.Column('id',sa.types.Integer,primary_key=True),
sa.Column('uuid',GUID,default=generate_uuid),
sa.Column('firstname',sa.types.String(32),nullable=False),
sa.Column('lastname',sa.types.String(32),nullable=False),
sa.Column('email',sa.types.String(100),nullable=False),
sa.Column('phone',sa.types.String(32)))
--
In a Pylons web app, I get:
class 'sqlalchemy.exc.ProgrammingError': (ProgrammingError) can't
adapt 'INSERT INTO contacts (id, uuid, firstname, lastname, email,
phone) VALUES (%(id)s, %(uuid)s, %(firstname)s, %(lastname)s, %
(email)s, %(phone)s)' {'uuid':
UUID('58d6bcb4-8cc6-11dd-983d-0016cb972e45'), 'firstname': u'Sean',
'lastname': u'Davis', 'email': u'sdavis2 AT mail.nih.gov', 'phone':
u'301-435-2652', 'id': 3L}
What am I missing?
Thanks,
Sean
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[sqlalchemy] Re: Custom type definition and can't adapt 'INSERT INTO.... error
On Sep 27, 5:16 pm, Michael Bayer [EMAIL PROTECTED] wrote:
On Sep 27, 2008, at 3:12 PM, Sean Davis wrote:
I have been playing with new types using sqlalchemy and have an error
I do not understand. Table schema and type definition are here:
-
def generate_uuid():
return uuid.uuid1()
class GUID(sa.types.TypeEngine):
def __init__(self):
pass
def get_col_spec(self):
return varchar(40)
def convert_bind_param(self, value, engine):
return str(value)
def convert_result_value(self, value, engine):
return uuid.UUID(value)
t_contacts = sa.Table('contacts',meta.metadata,
sa.Column('id',sa.types.Integer,primary_key=True),
sa.Column('uuid',GUID,default=generate_uuid),
sa.Column('firstname',sa.types.String(32),nullable=False),
sa.Column('lastname',sa.types.String(32),nullable=False),
sa.Column('email',sa.types.String(100),nullable=False),
sa.Column('phone',sa.types.String(32)))
--
In a Pylons web app, I get:
class 'sqlalchemy.exc.ProgrammingError': (ProgrammingError) can't
adapt 'INSERT INTO contacts (id, uuid, firstname, lastname, email,
phone) VALUES (%(id)s, %(uuid)s, %(firstname)s, %(lastname)s, %
(email)s, %(phone)s)' {'uuid':
UUID('58d6bcb4-8cc6-11dd-983d-0016cb972e45'), 'firstname': u'Sean',
'lastname': u'Davis', 'email': u'sdavis2 AT mail.nih.gov', 'phone':
u'301-435-2652', 'id': 3L}
assuming str(UUID()) returns a string, seems like your
convert_bind_param is not being called. This method was deprecated
throughout 0.4 and is removed in 0.5, so if you're on 0.5 you should
use the bind_processor() and result_processor() methods described
athttp://www.sqlalchemy.org/docs/05/types.html
Thanks. I had upgraded to 0.5 a while back and just came back to this
project and didn't make the connection that the types system had
changed.
Sean
.
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[sqlalchemy] Re: Column metadata from mapped class
On Jul 20, 11:28 am, Michael Bayer [EMAIL PROTECTED] wrote: On Jul 20, 2008, at 7:48 AM, Sean Davis wrote: I have been playing with 0.5 and have a very simple question. If I have a mapped class, User, how can I get at the columns of User? I see lots of constructs like User.c, but User has no 'c' attribute now. I am looking at finding the column types, names (to loop over), etc. theres a large section regarding this in the upgrade notes athttp://www.sqlalchemy.org/trac/wiki/05Migration , though its focused on rationale . The short answer for columns is to use the Table (i.e. sometable.c.somecolumn, for col in sometable.c:, etc). If you want to get the table for a mapped class if you don't have it already, say class_mapper(cls).mapped_table. Thanks, and sorry I didn't look at that doc before asking. That is exactly what I needed. Sean --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups sqlalchemy group. To post to this group, send email to sqlalchemy@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sqlalchemy?hl=en -~--~~~~--~~--~--~---
[sqlalchemy] Column metadata from mapped class
I have been playing with 0.5 and have a very simple question. If I have a mapped class, User, how can I get at the columns of User? I see lots of constructs like User.c, but User has no 'c' attribute now. I am looking at finding the column types, names (to loop over), etc. Thanks, Sean --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups sqlalchemy group. To post to this group, send email to sqlalchemy@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sqlalchemy?hl=en -~--~~~~--~~--~--~---
[sqlalchemy] Many-to-many back to single table
I have two tables: create table a ( id serial primary key, name varchar(255) unique ); create table b ( id serial primary key, subject int references a(id), object int references b(id), otherinfo varchar(255) ); I have been trying to pull ideas together from the self-referential portion of the manual and the many-to-many mapping section, and I haven't figured out how to go about coding this association table and referencing from table a to get subjects and objects of a given member of a. Is this possible to do? Thanks, Sean --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups sqlalchemy group. To post to this group, send email to sqlalchemy@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sqlalchemy?hl=en -~--~~~~--~~--~--~---
[sqlalchemy] Multiple foreign keys to the same table from another table
I have a table that has two columns that reference the same table in a
foreign-key relationship. What do I need to specify and where to
avoid the error below?
class 'sqlalchemy.exceptions.ArgumentError': Error determining
primary and/or secondary join for relationship 'FeatureLoc.feature
(Feature)'. If the underlying error cannot be corrected, you should
specify the 'primaryjoin' (and 'secondaryjoin', if there is an
association table present) keyword arguments to the relation()
function (or for backrefs, by specifying the backref using the
backref() function with keyword arguments) to explicitly specify the
join conditions. Nested error is Can't determine join between
'featureloc' and 'feature'; tables have more than one foreign key
constraint relationship between them. Please specify the 'onclause' of
this join explicitly.
I am reflecting these tables from the database:
feature_t = Table('feature',metadata,autoload=True)
featureloc_t = Table('featureloc',metadata,autoload=True)
class Feature(object):
pass
class FeatureLoc(object):
pass
sqlalchemy.orm.mapper(Feature,feature_t,properties={
'elements' : relation(Element,backref='feature')
})
sqlalchemy.orm.mapper(FeatureLoc,featureloc_t,properties={
'srcfeature' : relation(Feature),
'feature': relation(Feature)
})
Thanks,
Sean
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[sqlalchemy] Re: Multiple foreign keys to the same table from another table
On Jul 20, 11:57 pm, Sean Davis [EMAIL PROTECTED] wrote:
I have a table that has two columns that reference the same table in a
foreign-key relationship. What do I need to specify and where to
avoid the error below?
class 'sqlalchemy.exceptions.ArgumentError': Error determining
primary and/or secondary join for relationship 'FeatureLoc.feature
(Feature)'. If the underlying error cannot be corrected, you should
specify the 'primaryjoin' (and 'secondaryjoin', if there is an
association table present) keyword arguments to the relation()
function (or for backrefs, by specifying the backref using the
backref() function with keyword arguments) to explicitly specify the
join conditions. Nested error is Can't determine join between
'featureloc' and 'feature'; tables have more than one foreign key
constraint relationship between them. Please specify the 'onclause' of
this join explicitly.
I am reflecting these tables from the database:
feature_t = Table('feature',metadata,autoload=True)
featureloc_t = Table('featureloc',metadata,autoload=True)
class Feature(object):
pass
class FeatureLoc(object):
pass
sqlalchemy.orm.mapper(Feature,feature_t,properties={
'elements' : relation(Element,backref='feature')
})
sqlalchemy.orm.mapper(FeatureLoc,featureloc_t,properties={
'srcfeature' : relation(Feature),
'feature': relation(Feature)
})
Looks like this will do it:
sqlalchemy.orm.mapper(FeatureLoc,featureloc_t,properties={
'srcfeature' :
relation(Feature,primaryjoin=featureloc_t.c.srcfeature_id==feature_t.c.id,backref='features'),
'feature':
relation(Feature,primaryjoin=featureloc_t.c.feature_id==feature_t.c.id)
})
Sorry for the noise.
Sean
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[sqlalchemy] Re: save_or_update() with a unique but not primary key
On Tuesday 13 March 2007 07:35, Sean Davis wrote: We are creating a database that will have a set of autoincrement primary keys on the tables. However, many of the tables also have one or more unique keys associated with them. Can we use save_or_update() (and, by extension, cascade='save_or_update', etc.) by specifying one of the unique keys rather than specifying the primary key directly? Tried it. Looks like not. Sorry for the noise on the list. Sean --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups sqlalchemy group. To post to this group, send email to sqlalchemy@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sqlalchemy?hl=en -~--~~~~--~~--~--~---
[sqlalchemy] Re: Is it possible to know the size of a deferred PickleType?
On Tuesday 06 March 2007 05:32, Sanjay wrote: Hi All, Wondering if it is possible to know the size of a file stored in a deferred column (PickleType), without retrieving the file itself. I usually try to save the filesize as a separate column. Sean --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups sqlalchemy group. To post to this group, send email to sqlalchemy@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sqlalchemy?hl=en -~--~~~~--~~--~--~---
[sqlalchemy] Tool to autogenerate code from db schema
Just a quick question, but is there code available to autogenerate code for SA or Elixir from an existing (rather large) database? I could use SQLSoup directly, but it really helps me to be able to see the generated code. Also, some of the classes will benefit from some added methods. Thanks, Sean --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups sqlalchemy group. To post to this group, send email to sqlalchemy@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sqlalchemy?hl=en -~--~~~~--~~--~--~---
[sqlalchemy] Re: Is there any way to call a python function for primary key generation
On 2/13/07, vinjvinj [EMAIL PROTECTED] wrote: I use the mx.UID package to generate all my keys. Is there any way to specify that this function be called to generate the primary key for inserts? Thanks, Could this not be done on the database side (depends on the RDBMS)? Sean --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups sqlalchemy group. To post to this group, send email to sqlalchemy@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sqlalchemy?hl=en -~--~~~~--~~--~--~---
[sqlalchemy] schema comments
I looked over the docs but didn't find an answer (so the answer is probably no). Does SA allow descriptions (database comments) of tables and/or columns? Thanks, Sean --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups sqlalchemy group. To post to this group, send email to sqlalchemy@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sqlalchemy?hl=en -~--~~~~--~~--~--~---
[sqlalchemy] Re: Full Text Search using PostgreSQL and tsearch2
On Thursday 18 January 2007 07:11, Sanjay wrote: Hi All, Trying to implement full text search with PostgreSQL and tsearch2, being a beginner, I am facing some basic hurdles: 1. How to declare a table in SA, I mean, what SA datatype should tsvector correspond to? 2. Can the index be defined using SA, or we need to do it in the backend? 3. Can the trigger for auto update be defined using SA, or we need to do it in the backend? 4. How to frame the query in SA? SA doesn't support tsvectors, as far as I know. The simplest thing in my mind is to build one table that contains the tsvector (and is not mapped to SA) and a key to the original record. Then, you can do whatever queries you like (using the underlying database engine) to get keys to the data in the source table and use SA to grab these data. Not ideal, but I think it will work. Alternatively, you can create a new type for SA; there is a recent message in the archives about doing that (not with tsvector, but). As for querying, I'm not sure how that would be best implemented in SA. Sean --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups sqlalchemy group. To post to this group, send email to sqlalchemy@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sqlalchemy?hl=en -~--~~~~--~~--~--~---
[sqlalchemy] Re: Full Text Search using PostgreSQL and tsearch2
On Thursday 18 January 2007 14:19, Chris Shenton wrote: I'd be interested in how you work this out as I want to do something similar. Would you be willing to write it up and perhaps post it to the wiki? I was able to get MySQL's fulltext search working more quickly than PostgreSQL's and that's what my customer is used to so that's what I'm going to use for them. I haven't yet gotten to integrate it with SA. Down the road, I'd like to know how to do the same with PG. See here for at least an overview http://www.devx.com/opensource/Article/21674 There are other similar sites available via google. Sean --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups sqlalchemy group. To post to this group, send email to sqlalchemy@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sqlalchemy?hl=en -~--~~~~--~~--~--~---
[sqlalchemy] Accessing DBAPI cursor object from connection
I would like to access the underlying psycopg2 connection to get at a DBAPI2 cursor with the ultimate goal of using the copy_from/copy_to protocol for moving large amounts of data to/from the database. I can't seem to find a way to do that from a db engine or connection object. Is there a way (assuming that I am using postgres)? Thanks, Sean --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups sqlalchemy group. To post to this group, send email to sqlalchemy@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sqlalchemy?hl=en -~--~~~~--~~--~--~---
[sqlalchemy] Re: Accessing DBAPI cursor object from connection
On Thursday 18 January 2007 17:42, Jonathan Ellis wrote: engine.raw_connection().cursor() Ah, yes! Thanks. Sean On 1/18/07, Sean Davis [EMAIL PROTECTED] wrote: I would like to access the underlying psycopg2 connection to get at a DBAPI2 cursor with the ultimate goal of using the copy_from/copy_to protocol for moving large amounts of data to/from the database. I can't seem to find a way to do that from a db engine or connection object. Is there a way (assuming that I am using postgres)? Thanks, Sean --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups sqlalchemy group. To post to this group, send email to sqlalchemy@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sqlalchemy?hl=en -~--~~~~--~~--~--~---
[sqlalchemy] Oracle autoload problem?
I am experimenting with autoloading tables from Oracle (9.2) running on a
remote machine. Normal selects using cx_Oracle work just fine. Here is
what I get:
from sqlalchemy import *
eng = create_engine('oracle:// ...')
md = BoundMetaData(eng)
g2r = Table('gene2refseq',md,autoload=True)
Traceback (most recent call last):
File stdin, line 1, in module
File build/bdist.linux-x86_64/egg/sqlalchemy/schema.py, line 143, in
__call__
File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 505,
in reflecttable
File build/bdist.linux-x86_64/egg/sqlalchemy/databases/oracle.py, line
214, in reflecttable
File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 255,
in execute
File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 259,
in execute_text
File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 329,
in _execute_raw
File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 348,
in _execute
sqlalchemy.exceptions.SQLError: (DatabaseError) ORA-01008: not all variables
bound
'select distinct OWNER from ALL_TAB_COLUMNS where TABLE_NAME = :table_name'
{'table_name': 'GENE2REFSEQ'}
Any thoughts?
Thanks,
Sean
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[sqlalchemy] Re: Oracle autoload problem?
On 1/9/07, Andrija Zarić [EMAIL PROTECTED] wrote:
This very strange, because SQLAlchemy is issuing the query like it is
supposed to do. There is bind variable (table_name) but for some
reason cx_Oracle/Oracle is raising ORA-1008.
Can you assert that following is working:
import cx_Oracle as ora
e = ora.connect('...')
c = e.cursor()
c.execute(select distinct OWNER from ALL_TAB_COLUMNS where
TABLE_NAME = :table_name,{'table_name':'GENE2REFSEQ'})
c.fetchall()
I'm using autoload feature with Oracle 8.1.7 and 10XE, both tables
with unique name and same name with multiple owners without any
problems. SQLAlchemy is from svn trunk and cx_Oracle is 4.1
cx_Oracle indeed looks to be the issue. I'll sort it out in more detail,
but bound parameters are not working for me in any queries I have tried. It
works otherwise, but not with bind params.
Sean
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[sqlalchemy] Lazy load a single column
A simple question: I have a table with one HUGE column. Is there a way to make this column lazy-loaded? Thanks, Sean --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups sqlalchemy group. To post to this group, send email to sqlalchemy@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sqlalchemy?hl=en -~--~~~~--~~--~--~---
[sqlalchemy] Re: Lazy load a single column
On 1/5/07, Lee McFadden [EMAIL PROTECTED] wrote: On 1/5/07, Sean Davis [EMAIL PROTECTED] wrote: A simple question: I have a table with one HUGE column. Is there a way to make this column lazy-loaded? http://www.sqlalchemy.org/docs/adv_datamapping.myt#advdatamapping_properties_deferred Perfect! Thanks. Sean --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups sqlalchemy group. To post to this group, send email to sqlalchemy@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sqlalchemy?hl=en -~--~~~~--~~--~--~---
[sqlalchemy] SqlSoup error
I have the following three tables and trying to do a join. See below for
details:
g_main (
gene_id serial primary key,
.
);
g_refseq (
refseq varchar references refseq(refseq),
gene_id int references g_main(gene_id)
);
refseq (
refseq varchar primary key
);
from sqlalchemy.ext.sqlsoup import SqlSoup
db = SqlSoup('postgres://user:[EMAIL PROTECTED]/annodb4')
genes = db.g_main.select_by(symbol='ADAM12')
len(genes)
2
refseqs = db.g_refseq.select_by(gene_id=672)
len(refseqs)
13
join1 = db.join(db.g_main,db.g_refseq)
Traceback (most recent call last):
File stdin, line 1, in module
File build/bdist.linux-x86_64/egg/sqlalchemy/ext/sqlsoup.py, line 410, in
join
File build/bdist.linux-x86_64/egg/sqlalchemy/ext/sqlsoup.py, line 402, in
map
File build/bdist.linux-x86_64/egg/sqlalchemy/ext/sqlsoup.py, line 369, in
class_for_table
File build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py, line 19, in
__init__
File build/bdist.linux-x86_64/egg/sqlalchemy/orm/mapper.py, line 252, in
compile
File build/bdist.linux-x86_64/egg/sqlalchemy/orm/mapper.py, line 270, in
_compile_all
File build/bdist.linux-x86_64/egg/sqlalchemy/orm/mapper.py, line 497, in
_initialize_properties
AttributeError: 'Mapper' object has no attribute '_Mapper__props'
I am using:
SQLAlchemy-0.3.3-py2.5.egg
Any suggestions on what I am missing?
Thanks,
Sean
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[sqlalchemy] Re: SqlSoup error
On Friday 22 December 2006 10:10, Alan Franzoni wrote: Any suggestions on what I am missing? I don't use sqlsoup and I don't know whether you not using it correctly; btw, if you're in hurry, as a simple workaround, I suggest you add this line to sqlsoup.py, line 369, just above klass_query =... : klass._mapper.compile() and see if it works. Alan, This was, indeed, the fix. And, to clarify for Michael, I did include a primary key on the g_refseq table but neglected to include it in the table def--sorry for being misleading. Thanks for the help. Sean --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups sqlalchemy group. To post to this group, send email to sqlalchemy@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sqlalchemy?hl=en -~--~~~~--~~--~--~---
[sqlalchemy] Re: Misunderstanding something with autoloading
On Tuesday 19 December 2006 05:51, Alan Franzoni wrote:
from sqlalchemy import *
db = create_engine('postgres://user:[EMAIL PROTECTED]/test5')
metadata = BoundMetaData(db)
tb = Table('gffdata',metadata,autoload=True)
This works fine on my system (ubuntu edgy, x86, python 2.5, postgresql
8.1.4, psycopg 2.0.5, SA 0.3.3), could you please post the details of
yours?
Thanks for trying it. I am on openSUSE 10.2 x86_64, postgres 8.2 (running
remotely on an Apple XServer), psycopy2.0.5.1, SA 0.3.3.
I played a bit more and it happens only with a particular database. When
connecting to another database, it seems to work just fine. I'll look into
it more here, as it seems to be idiosyncratic. If I come to any hard
conclusions, I'll forward them along.
Sean
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[sqlalchemy] Misunderstanding something with autoloading
I have a simple test case given here:
from sqlalchemy import *
db = create_engine('postgres://user:[EMAIL PROTECTED]/test5')
metadata = BoundMetaData(db)
tb = Table('gffdata',metadata,autoload=True)
Up to this point, I think this looks like what is in the tutorial. However, I
get the following error when trying to autoload.
Traceback (most recent call last):
File stdin, line 1, in module
File build/bdist.linux-x86_64/egg/sqlalchemy/schema.py, line 143, in
__call__
File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 505, in
reflecttable
File build/bdist.linux-x86_64/egg/sqlalchemy/databases/postgres.py, line
386, in reflecttable
TypeError: __init__() takes at most 2 arguments (3 given)
metadata.get_engine().raw_connection
bound method Engine.raw_connection of sqlalchemy.engine.base.Engine object
at 0x9168d0
But after I do this call, I can autoload the table without problem.
tb = Table('gffdata',metadata,autoload=True)
And selecting, etc., works fine at this point. What am I missing?
Thanks,
Sean
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